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Markov model

Laure-Anne Van Bellinghen, Alen Marijam, Gabriela Tannus Araujo, Jorge Gomez, Ilse Van Vlaenderen
BACKGROUND: Influenza burden in Brazil is considerable with 4.2-6.4 million cases in 2008 and influenza-like-illness responsible for 16.9% of hospitalizations. Cost-effectiveness of influenza vaccination may be assessed by different types of models, with limitations due to data availability, assumptions, and modelling approach. OBJECTIVE: To understand the impact of model complexity, the cost-utility of quadrivalent versus trivalent influenza vaccines (QIV versus TIV) in Brazil was estimated using three distinct models: a 1-year decision tree population model with three age groups (FLOU); a more detailed 1-year population model with five age groups (FLORA); and a more complex lifetime multi-cohort Markov model with nine age groups (FLORENCE)...
January 17, 2018: Brazilian Journal of Infectious Diseases
Gong Chen, Weina Xu, Diannan Lu, Jianzhong Wu, Zheng Liu
Enzyme immobilization with a nanostructure material can enhance its stability and facilitate reusability. However, the apparent activity is often compromised due to additional diffusion barriers and complex interactions with the substrates and solvent molecules. The present study elucidates the effects of the surface hydrophobicity of nano-confinement on CO2 diffusion to the active site of human carbonic anhydrase II (CA), an enzyme that is able to catalyze CO2 hydration at extremely high turnover rates. Using the Markov-state model in combination with coarse-grained molecular dynamics simulations, we demonstrate that a hydrophobic cage increases CO2 local density but hinders its diffusion towards the active site of CA under confinement...
January 21, 2018: Journal of Chemical Physics
Dolly Han, Nicolas Iragorri, Fiona Clement, Diane Lorenzetti, Eldon Spackman
BACKGROUND: Chronic constipation (CC) has a significant impact on patients' quality of life and imposes an economic burden on individuals and the healthcare system. Treatment options include dietary changes, lifestyle modifications, fibre supplements, stool softeners, and laxatives. OBJECTIVE: We undertook this systematic review to comprehensively evaluate the cost effectiveness of treatments for CC. METHODS: We searched ten common databases to identify economic evaluations published to 13 June 2017...
January 19, 2018: PharmacoEconomics
Bart de Boer, Bill Thompson
Language is the result of two concurrent evolutionary processes: biological and cultural inheritance. An influential evolutionary hypothesis known as the moving target problem implies inherent limitations on the interactions between our two inheritance streams that result from a difference in pace: the speed of cultural evolution is thought to rule out cognitive adaptation to culturally evolving aspects of language. We examine this hypothesis formally by casting it as as a problem of adaptation in time-varying environments...
January 19, 2018: Scientific Reports
Maurizio Righini, Antony Lee, Cristhian Cañari-Chumpitaz, Troy Lionberger, Ronen Gabizon, Yves Coello, Ignacio Tinoco, Carlos Bustamante
In recent years, highly stable optical tweezers systems have enabled the characterization of the dynamics of molecular motors at very high resolution. However, the motion of many motors with angstrom-scale dynamics cannot be consistently resolved due to poor signal-to-noise ratio. Using an acousto-optic deflector to generate a "time-shared" dual-optical trap, we decreased low-frequency noise by more than one order of magnitude compared with conventional dual-trap optical tweezers. Using this instrument, we implemented a protocol that synthesizes single base-pair trajectories, which are used to test a Large State Space Hidden Markov Model algorithm to recover their individual steps...
January 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
Zurab Bzhalava, Emilie Hultin, Joakim Dillner
When human samples are sequenced, many assembled contigs are "unknown", as conventional alignments find no similarity to known sequences. Hidden Markov models (HMM) exploit the positions of specific nucleotides in protein-encoding codons in various microbes. The algorithm HMMER3 implements HMM using a reference set of sequences encoding viral proteins, "vFam". We used HMMER3 analysis of "unknown" human sample-derived sequences and identified 510 contigs distantly related to viruses (Anelloviridae (n = 1), Baculoviridae (n = 34), Circoviridae (n = 35), Caulimoviridae (n = 3), Closteroviridae (n = 5), Geminiviridae (n = 21), Herpesviridae (n = 10), Iridoviridae (n = 12), Marseillevirus (n = 26), Mimiviridae (n = 80), Phycodnaviridae (n = 165), Poxviridae (n = 23), Retroviridae (n = 6) and 89 contigs related to described viruses not yet assigned to any taxonomic family)...
2018: PloS One
James N Laditka, Sarah B Laditka
The United States workforce is aging. At the same time more people have chronic conditions, for longer periods. Given these trends the importance of work disability, physical or nervous problems that limit a person's type or amount of work, is increasing. No research has examined transitions among multiple levels of work disability, recovery from work disability, or trends. Limited research has focused on work disability among African Americans and Hispanics, or separately for women and men. We examined these areas using data from 30,563 adults in the 1968-2015 Panel Study of Income Dynamics...
April 2018: SSM—Population Health
David B Saakian
We write a master equation for the distributions related to hidden Markov processes (HMPs) and solve it using a functional equation. Thus the solution of HMPs is mapped exactly to the solution of the functional equation. For a general case the latter can be solved only numerically. We derive an exact expression for the entropy of HMPs. Our expression for the entropy is an alternative to the ones given before by the solution of integral equations. The exact solution is possible because actually the model can be considered as a generalized random walk on a one-dimensional strip...
November 2017: Physical Review. E
Jannik Ehrich, Andreas Engel
Systems with interacting degrees of freedom play a prominent role in stochastic thermodynamics. Our aim is to use the concept of detached path probabilities and detached entropy production for bipartite Markov processes and elaborate on a series of special cases including measurement-feedback systems, sensors, and hidden Markov models. For these special cases we show that fluctuation theorems involving the detached entropy production recover known results which have been obtained separately before. Additionally, we show that the fluctuation relation for the detached entropy production can be used in model selection for data stemming from a hidden Markov model...
October 2017: Physical Review. E
S S Melnik, O V Usatenko
The main goal of this paper is to develop an estimate for the conditional probability function of random stationary ergodic symbolic sequences with elements belonging to a finite alphabet. We elaborate on a decomposition procedure for the conditional probability function of sequences considered to be high-order Markov chains. We represent the conditional probability function as the sum of multilinear memory function monomials of different orders (from zero up to the chain order). This allows us to introduce a family of Markov chain models and to construct artificial sequences via a method of successive iterations, taking into account at each step increasingly high correlations among random elements...
July 2017: Physical Review. E
Victor Herdeiro
A numerical method was recently proposed in Herdeiro and Doyon [Phys. Rev. E 94, 043322 (2016)10.1103/PhysRevE.94.043322] showing a precise sampling of the infinite plane two-dimensional critical Ising model for finite lattice subsections. The present note extends the method to a larger class of models, namely the O(n) loop gas models for n∈(1,2]. We argue that even though the Gibbs measure is nonlocal, it is factorizable on finite subsections when sufficient information on the loops touching the boundaries is stored...
July 2017: Physical Review. E
Or Alus, Shmuel Fishman, James D Meiss
We compute universal distributions for the transition probabilities of a Markov model for transport in the mixed phase space of area-preserving maps and verify that the survival probability distribution for trajectories near an infinite island-around-island hierarchy exhibits, on average, a power-law decay with exponent γ=1.57. This exponent agrees with that found from simulations of the Hénon and Chirikov-Taylor maps. This provides evidence that the Meiss-Ott Markov tree model describes the transport for mixed systems...
September 2017: Physical Review. E
Xin Wang, Weihua Li, Longzhao Liu, Sen Pei, Shaoting Tang, Zhiming Zheng
For information diffusion in multiplex networks, the effect of interlayer contagion on spreading dynamics has been explored in different settings. Nevertheless, the impact of interlayer recovery processes, i.e., the transition of nodes to stiflers in all layers after they become stiflers in any layer, still remains unclear. In this paper, we propose a modified ignorant-spreader-stifler model of rumor spreading equipped with an interlayer recovery mechanism. We find that the information diffusion can be effectively promoted for a range of interlayer recovery rates...
September 2017: Physical Review. E
Victor Herdeiro
Herdeiro and Doyon [Phys. Rev. E 94, 043322 (2016)2470-004510.1103/PhysRevE.94.043322] introduced a numerical recipe, dubbed uv sampler, offering precise estimations of the conformal field theory (CFT) data of the planar two-dimensional (2D) critical Ising model. It made use of scale invariance emerging at the critical point in order to sample finite sublattice marginals of the infinite plane Gibbs measure of the model by producing holographic boundary distributions. The main ingredient of the Markov chain Monte Carlo sampler is the invariance under dilation...
September 2017: Physical Review. E
Jean-Gabriel Young, Giovanni Petri, Francesco Vaccarino, Alice Patania
Simplicial complexes are now a popular alternative to networks when it comes to describing the structure of complex systems, primarily because they encode multinode interactions explicitly. With this new description comes the need for principled null models that allow for easy comparison with empirical data. We propose a natural candidate, the simplicial configuration model. The core of our contribution is an efficient and uniform Markov chain Monte Carlo sampler for this model. We demonstrate its usefulness in a short case study by investigating the topology of three real systems and their randomized counterparts (using their Betti numbers)...
September 2017: Physical Review. E
David J Jörg
We present a generalization of the Kuramoto phase oscillator model in which phases advance in discrete phase increments through Poisson processes, rendering both intrinsic oscillations and coupling inherently stochastic. We study the effects of phase discretization on the synchronization and precision properties of the coupled system both analytically and numerically. Remarkably, many key observables such as the steady-state synchrony and the quality of oscillations show distinct extrema while converging to the classical Kuramoto model in the limit of a continuous phase...
September 2017: Physical Review. E
Chen Jia
Here we develop an effective approach to simplify two-time-scale Markov chains with infinite state spaces by removal of states with fast leaving rates, which improves the simplification method of finite Markov chains. We introduce the concept of fast transition paths and show that the effective transitions of the reduced chain can be represented as the superposition of the direct transitions and the indirect transitions via all the fast transition paths. Furthermore, we apply our simplification approach to the standard Markov model of single-cell stochastic gene expression and provide a mathematical theory of random gene expression bursts...
September 2017: Physical Review. E
Nathan K Itoga, Hataka R Minami, Meenadachi Chelvakumar, Keon Pearson, Matthew M Mell, Eran Bendavid, Douglas K Owens
Screening for asymptomatic peripheral artery disease (aPAD) with the ankle-brachial index (ABI) test is hypothesized to reduce disease progression and cardiovascular (CV) events by identifying individuals who may benefit from early initiation of medical therapy. Using a Markov model, we evaluated the cost effectiveness of initiating medical therapy (e.g. statin and ACE-inhibitor) after a positive ankle-brachial index (ABI) screen in 65-year-old patients. We modeled progression to symptomatic PAD (sPAD) and CV events with and without ABI screening, evaluating differences in costs and quality-adjusted life years (QALYs)...
January 1, 2018: Vascular Medicine
James C Ulchaker, Melissa S Martinson
Objective: To conduct a cost-effectiveness analysis from payers' perspectives of six treatments for lower urinary tract symptoms (LUTS) associated with benign prostatic hyperplasia (BPH) and to examine positioning of these modalities in the marketplace for the best use of health care funds and quality-of-life benefits for patients. Methods: The economic analysis was conducted with a Markov model to compare combination prescription drug therapy (ComboRx), minimally invasive therapies (MITs) including convective radiofrequency (RF) water vapor thermal therapy (Rezūm®), conductive RF thermal therapy (Prostiva®), and prostatic urethral lift (UroLift®), and invasive surgical procedures including photovaporization of the prostate (Greenlight® PVP) and transurethral resection of the prostate (TURP)...
2018: ClinicoEconomics and Outcomes Research: CEOR
Noelia Ferruz, Stefan Doerr, Michelle A Vanase-Frawley, Yaozhong Zou, Xiaomin Chen, Eric S Marr, Robin T Nelson, Bethany L Kormos, Travis T Wager, Xinjun Hou, Anabella Villalobos, Simone Sciabola, Gianni De Fabritiis
The recent increase in the number of X-ray crystal structures of G-protein coupled receptors (GPCRs) has been enabling for structure-based drug design (SBDD) efforts. These structures have revealed that GPCRs are highly dynamic macromolecules whose function is dependent on their intrinsic flexibility. Unfortunately, the use of static structures to understand ligand binding can potentially be misleading, especially in systems with an inherently high degree of conformational flexibility. Here, we show that docking a set of dopamine D3 receptor compounds into the existing eticlopride-bound dopamine D3 receptor (D3R) X-ray crystal structure resulted in poses that were not consistent with results obtained from site-directed mutagenesis experiments...
January 17, 2018: Scientific Reports
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